Man-Machine Phased-Mission System (MMPMS) usually demands the cooperation of operators with different responsibilities and machines to accomplish multi-phase missions. Its machine configuration and human organization structure may change across phases, and phase dependencies of machine failures and human errors may exist. In current studies, the safety of man-machine system is usually analyzed qualitatively by System Theoretic Process Analysis (STPA) and assessed quantitatively by the integration of STPA with Bayesian Networks (BN). These studies only focus on single-phase systems and conduct single-phase BN while cannot address the features of MMPMS. In this paper, a qualitative analysis and quantitative assessment method for phase dependencies is proposed and integrated into the method that combines STPA and BN. Firstly, four types of phase dependencies in MMPMS are identified. Secondly, new mapping rules for phase dependencies are proposed to integrate single-phase BN into a multi-phase BN. Thirdly, the quantitative assessment method for phase dependencies considering the effects of human organization structure changes are proposed to quantify the parameters of multi-phase BN. Fourthly, the safety of MMPMS can be assessed through multi-phase BN. Finally, an Unmanned Aerial Vehicle system with three-phase missions is presented as a case study to demonstrate the effectiveness of the proposed method.